Do I need spearate files for different editions of Magento? (ie Enterprise or Community)
Just transfer over the files and you're good. There are no extra instructions for enterprise, professional or community editions. We make sure to program the code so that it works with all full editions of Magento (not Magento GO yet). They programmed their core so that this could be done, so it's a bit sad that other extension providers don't take advantage of this.
Theme files are all in the default/default directory. Magento will fall to default/default before hitting default/base, so you're good.